Introduction and Objective: Chromatin-associated regulatory RNAs (carRNAs), including promoter- and enhancer-associated RNAs, are known regulators of global gene transcription, yet the regulation of carRNAs remains poorly understood. Recent studies implicate RNA N6-methyladenosine (m6A) modification in carRNA stability and function. Seminal work from our lab has shown that m6A “writers” (e.g., methyltransferase-like 3 (METTL3) and METTL14) are downregulated in islets of individuals with type 2 diabetes (T2D), leading to altered m6A landscapes that better segregate T2D from control samples compared to the transcriptome. Here we report the role of m6A in regulating carRNAs in human T2D islets.Methods: Total chromatin-associated RNA (caRNA) was isolated from human islets (n=14 Control; n=8 T2D) and characterized using RNA sequencing. m6A methylation profiles were assessed by methylated RNA immunoprecipitation sequencing (MeRIP-seq). Validation was performed in the EndoC-βH1 human β-cell line following knockdown of METTL3 or METTL14.Results: We identified over 700 differentially regulated caRNAs in T2D islets, with functional enrichment revealing downregulated caRNAs involved in metabolism and oxidation, and upregulated caRNAs regulating RNA biology processes. MeRIP-seq revealed hypomethylation of key regulatory carRNAs, such as lncRNAs and promoter-associated RNAs, in T2D. In EndoC-βH1 cells, METTL3/14 knockdown similarly dysregulated caRNAs and downregulated β-cell identity pathways, while upregulating RNA processing and transcription pathways (n=4; FDR<0.05).Conclusion: Our findings provide novel insights into the epigenetic regulation of β-cell biology in T2D. The differential expression and m6A modification of carRNAs in T2D islets highlight their potential role in β-cell dysfunction and offer new therapeutic targets to modulate β-cell identity and insulin secretion.
N. Shukla: None. C. Ju: None. H. Li: None. C. He: None. R. Kulkarni: Advisory Panel; Novo Nordisk, Biomea Fusion, REDD Pharma, Inversago Pharma. Research Support; Inversago Pharma. Stock/Shareholder; Biomea Fusion.
National Institute of Health (R01 DK067536)
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